Quantitative determination of gene strand bias in prokaryotic genomes.

Most prokaryotic genomes display strand compositional asymmetries, but the reasons for these biases remain unclear. When the distribution of gene orientation is biased, as it often is, this may induce a bias in composition, as codon frequencies are…

Gene order in prokaryotes is conserved to a much lesser extent than protein sequences. Only some operons, primarily those that encode physically interacting proteins, are conserved in all or most of the bacterial and archaeal genomes. Nevertheless,…

We present 'gene prediction improvement pipeline' (GenePRIMP; http://geneprimp.jgi-psf.org/), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start…

Molecular genetics, which has its roots mainly in the development of microbial genetics in the middle of this century, not only greatly facilitates investigations of essential cellular functions, but also offers a means to better understand…

A computational method was developed for delineating connected gene neighborhoods in bacterial and archaeal genomes. These gene neighborhoods are not typically present, in their entirety, in any single genome, but are held together by overlapping,…

Insertion sequences (ISs) are small DNA segments that are often capable of moving neighbouring genes. Over 1500 different ISs have been identified to date. They can have large and spectacular effects in shaping and reshuffling the bacterial genome.…

DNA curvature is known to play a biological role in gene regulation, in particular, initiation of transcription. We applied the software CURVATURE based on the wedge model to predict whether promoter regions of certain prokaryotes may be…

Prokaryotic genomics is shifting towards comparative approaches to unravel how and why genomes change over time. Both phylogenetic and population genetics approaches are required to dissect the relative roles of selection and drift under these…

Background: The integration of genomic information with quantitative experimental data is a key component of systems biology. An increasing number of microbial genomes are being sequenced, leading to an increasing amount of data from post-genomics…

Eight new microbial genomes have been published since the last Genome Update column was written. The collection of this months genomes is shown in Table 1. The published genomes represent four bacterial phyla: one from the Actinobacteria…